A5034588960- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Plant Molecular Biology Research
- Plant Reproductive Biology
- Bioinformatics and Genomic Networks
- Astro and Planetary Science
- Space Satellite Systems and Control
- Plant nutrient uptake and metabolism
- Spacecraft Design and Technology
- Greenhouse Technology and Climate Control
- Spacecraft and Cryogenic Technologies
- Light effects on plants
- GNSS positioning and interference
- Software System Performance and Reliability
- Planetary Science and Exploration
- Protein Structure and Dynamics
- Spacecraft Dynamics and Control
- Online Learning and Analytics
- Artificial Intelligence in Healthcare
- Fungal and yeast genetics research
- Calibration and Measurement Techniques
- Evolution and Genetic Dynamics
- Scientific Computing and Data Management
- Modeling and Simulation Systems
- Connexins and lens biology
University of Florida
2022
California State University, Northridge
2013-2020
California Institute of Technology
1993-2013
California State University System
2013
Jet Propulsion Laboratory
1998-2006
Lund University
2006
University of California, Irvine
2006
Ford Motor Company (United States)
1988
Drexel University
1982
Abstract Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the biology community needs information standards if models are be shared, evaluated and developed cooperatively. Results: We summarize Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is software-independent language describing common research in many areas of computational biology, including cell...
Most of the published quantitative models in biology are lost for community because they either not made available or insufficiently characterized to allow them be reused. The lack a standard description format, stringent reviewing and authors' carelessness main causes incomplete model descriptions. With today's increased interest detailed biochemical models, it is necessary define minimum quality encoding those models. We propose set rules curating biological systems. These procedures...
Recent studies show that plant organ positioning may be mediated by localized concentrations of the hormone auxin. Auxin patterning in shoot apical meristem is turn brought about subcellular polar distribution putative auxin efflux mediator, PIN1. However, question what signals determine PIN1 polarization and how this gives rise to regular patterns concentration remains unknown. Here we address these questions using mathematical modeling combined with confocal imaging. We propose a model...
Motivation: The above-ground tissues of higher plants are generated from a small region cells situated at the plant apex called shoot apical meristem. An important genetic control circuit modulating size Arabidopsis thaliana meristem is feed-back network between CLAVATA3 and WUSCHEL genes. Although expression patterns for these genes do not overlap, activity both necessary sufficient (when expressed ectopically) induction expression. However, upregulation in conjunction with receptor kinase...
Significance Plant cells are incapable of sliding past each other, so generation shape and structure in plant tissue is dependent on dividing expanding particular directions. Therefore, understanding how choose where to build new walls critical patterned. In the present study we expand previous models cell division further understand what parameters geometry growth influence position walls.
Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions transcriptional activation. Multi-compartment systems are represented as graphs STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric connectionist models. Reactions translated into differential equations can be solved numerically generate predictive time courses or output of that...
Abstract Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into data structures and provides platform evaluating these Once model read by MathSBML, it fully compatible with standard functions such as NDSolve (a differential-algebraic equations solver). also an application programming interface viewing, manipulating, running numerical simulations; exporting models; converting in to other formats, XPP,...
Abstract Motivation: As a first step toward the elucidation of systems biology complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in processes such as signal transduction metabolic pathways. Results: We describe kMech, Cellerator language extension describes suite mechanisms. Each mechanism is parsed by kMech into set fundamental association–dissociation reactions are translated ordinary differential...
As a first step toward the elucidation of systems biology model organism Escherichia coli, it was our goal to mathematically metabolic system intermediate complexity, namely well studied end product-regulated pathways for biosynthesis branched chain amino acids l-isoleucine, l-valine, and l-leucine. This has been accomplished with use kMech (Yang, C.-R., Shapiro, B. E., Mjolsness, E. D., Hatfield, G. W. (2005) Bioinformatics 21, in press), Cellerator (Shapiro, Levchenko, A., Meyerowitz, M.,...
Cellzilla is a two-dimensional tissue simulation platform for plant modeling utilizing Cellerator arrows. describes biochemical interactions with simplified arrow-based notation; all are input as reactions and automatically translated to the appropriate differential equations using computer algebra system. Cells represented by polygonal mesh of well-mixed compartments. Cell constituents can interact intercellularly via diffusion, transport, action at distance, well amongst themselves within...
In our effort to elucidate the systems biology of model organism, Escherichia coli, we have developed a mathematical that simulates allosteric regulation for threonine biosynthesis pathway starting from aspartate. To achieve this goal, used kMech, Cellerator language extension describes enzyme mechanisms modeling metabolic pathways. These are converted by into ordinary differential equations (ODEs) solvable Mathematica™. paper, describe more flexible in Cellerator, which generalizes Monod,...
Ergosterol was identified as the major free sterol of Aspergillus nidulans by thin-layer chromatography, alumina column gas-liquid high-performance liquid UV spectroscopy, proton magnetic resonance spectroscopy and mass spectral analysis. Lanosterol, initial cyclized precursor ergosterol, a minor component sterols. In steryl ester material, however, lanosterol usually more abundant than suggesting that esters serve storage compounds for membrane precursors.
The shoot apical meristem (SAM) is a dome-shaped collection of cells at the apex growing plants from which all above-ground tissue ultimately derives. In Arabidopsis thaliana (thale cress), small flowering weed Brassicaceae family (related to mustard and cabbage), SAM typically contains some three five hundred that range ten microns in diameter. These are organized into several distinct zones maintain their topological functional relationships throughout life plant. As plant grows, organs...
With pressure to increase graduation rates and reduce time degree in higher education, it is important identify at-risk students early. Automated early warning systems are therefore highly desirable. In this paper, we use unsupervised clustering techniques predict the status of declared majors five departments at California State University Northridge (CSUN), based on a minimal number lower division courses each major. addition, detected clusters hidden bottleneck courses.